Journal: Cell reports

Article Title: Principles of assembly and regulation of condensates of Polycomb repressive complex 1 through phase separation

doi: 10.1016/j.celrep.2023.113136

Figure Lengend Snippet: (A) A hypothetical model describing how condensate composition regulates the partitioning of CBX2-PRC1 components and nucleosomes and the exchange properties of the scaffold CBX2. Colored hexagons are the CBX2-PRC1 clients (magenta) and nucleosomes (green). (B) Representative epi-fluorescence images of CBX2-PRC1 subunits in the four-component (CBX2, RING1B [R], MEL18 [M], and PHC1 [P]) system. Scale bars, 5.0 μm. (C) Box plot of condensed fraction in the four-component system quantified from (B). p value is calculated using Student’s t test (*p < 0.05; **p < 0.01). (D) FRAP curves of CBX2 in the single-component, two-component, three-component, and four-component systems. Error bars denote SD. (E) Example confocal fluorescence images of CBX2 and nucleosomes (Nuc.) in the two-component, three-component, four-component, and five-component systems. Scale bars, 5.0 μm. (F) Box plot of condensed fraction of CBX2 and nucleosomes quantified from (E). p value is calculated using Student’s t test (**p < 0.01). (G) FRAP curves of YFP-CBX2 in the two-, three-, four-, and five-component systems. Error bars denote SD. (H) Representative live-cell epi-fluorescence images of HT-CBX2 in wild-type (WT), Ring1a −/− /b −/− , and Bmi1 −/− /Mel18 −/− mESC lines. Scale bars, 5.0 μm. (I and J) Box plots of condensed fraction (I) and size (J) of HT-CBX2 condensates quantified from (H). p value is calculated using Student’s t test (**p < 0.01). Error bars denote SD. (K) Example confocal images of FRAP of HT-CBX2 in wild-type (WT), Ring1a −/− /b −/− , and Bmi1 −/− /Mel18 −/− mESC lines. Red arrows show condensates to be bleached. Scale bar, 5.0 μm. (L) FRAP curves of HT-CBX2 within and outside condensates in wild-type (WT), Ring1a −/− /b −/− , and Bmi1 −/− /Mel18 −/− mESC lines. Error bars denote SD.

Article Snippet: The FRAP curves were fitted by a single-exponential function implemented in OriginLab as described in. (Equation 5) I = r − m ⋅ e ( − k ⋅ t ) Where m is the mobile fraction.

Techniques: Fluorescence

Journal: PLoS ONE

Article Title: Recombinant hTRBP and hPACT Modulate hAgo2-Catalyzed siRNA-Mediated Target RNA Cleavage In Vitro

doi: 10.1371/journal.pone.0146814

Figure Lengend Snippet: Representative stopped-flow graphs are shown. The inserts show the reaction on a shorter time scale. 50 nM fluorescently labeled double-stranded siRNA (aslam-FAM/slam) were rapidly mixed with 500 nM hTRBP (A) or hPACT (B). Data were fitted to a double exponential equation yielding the following rates: k 1 : 11.1 (± 2.3) s -1 and k 2 : 0.02 (± 0.001) s -1 for hTRBP and k 1 : 37.8 (± 2.5) s -1 and k 2 : 0.04 (± 0.005) s -1 for hPACT.

Article Snippet: Data were fitted using a single exponential equation (Grafit 5, Erithacus Software).

Techniques: Labeling

Journal: PLoS ONE

Article Title: Recombinant hTRBP and hPACT Modulate hAgo2-Catalyzed siRNA-Mediated Target RNA Cleavage In Vitro

doi: 10.1371/journal.pone.0146814

Figure Lengend Snippet: The different substrate combinations (ss-siRNA & long target, ds-siRNA & long target, ds-siRNA or ss-siRNA & short target) are depicted as little cartoons on top of the corresponding graph. For target RNA cleavage either 2.5 nM radioactively labeled ICAM-1-IVT (A, B) or s2b (D) were mixed with binary complexes consisting of either 100 nM as2b (A, D) or as2b/s2b (B) and 3 μM hAgo2 in the absence (open circles) or presence of 3 μM hTRBP (closed circles), hTRBP-D12 (open squares) and hPACT (closed squares), respectively. For ds-siRNA cleavage, i.e. passenger cleavage (C), 30 nM 5’-32P-passenger labeled siRNA (as2b/s2b) was mixed with 3 μM hAgo2 in the presence or absence of dsRBPs as described above. Samples were taken at different time points, analyzed by denaturing PAGE (8% for ICAM-1-IVT and 20% for s2b) and detected by autoradiography (Figure H in ). Data shown are averaged from at least three independent measurements. Error bars represent standard deviation. Experimental data were fitted to an exponential equation. Rate constants and corresponding amplitudes are listed in .

Article Snippet: Data were fitted using a single exponential equation (Grafit 5, Erithacus Software).

Techniques: Labeling, Autoradiography, Standard Deviation

Journal: PLoS ONE

Article Title: Recombinant hTRBP and hPACT Modulate hAgo2-Catalyzed siRNA-Mediated Target RNA Cleavage In Vitro

doi: 10.1371/journal.pone.0146814

Figure Lengend Snippet: Representative stopped-flow graphs are shown. Ternary complexes composed of 500 nM hAgo2, 20 nM guide RNA (as2b-FAM) and 40 nM target RNA (s2b) were preassembled and subsequently rapidly mixed with 2 μM unlabeled guide RNA and 500 nM hTRBP-D12 (A) or hTRBP (B). In both cases data could be best fitted using a triple exponential equation, yielding the following rate constants: (A) k -1 : 18.4 (± 1.2) s -1 , k -2 : 0.1 (± 0.007) s -1 , k -3 : 0.002 (± 0.0005) s -1 and (B) k -1 : 15.9 (± 4.6) s -1 , k -2 : 0.05 (± 0.001) s -1 , k -3 : 0.0005 (± 0.0002) s -1 . Rate constants are summarized in .

Article Snippet: Data were fitted using a single exponential equation (Grafit 5, Erithacus Software).

Techniques:

Journal: PLoS ONE

Article Title: Recombinant hTRBP and hPACT Modulate hAgo2-Catalyzed siRNA-Mediated Target RNA Cleavage In Vitro

doi: 10.1371/journal.pone.0146814

Figure Lengend Snippet: Representative stopped-flow graphs are shown. The inserts show the reaction on a shorter time scale. 20 nM of fluorescently labeled double-stranded siRNA (as2b-FAM/s2B) were pre-incubated with 600 nM hTRBP (A, C) or hPACT (B, D). The binary complexes were subsequently rapidly mixed with either hAgo2 (400 nM in case of A and 600 nM in case of B) or 600 nM hAgo2-PAZ9 (C, D). Data were fitted to an exponential equation. For hAgo2 & hTRBP: k 1 : 28.8 (± 10.8) s -1 , k 2 : 0.33 (±0.03) s -1 and k 3 : 0.002 (± 0.0001) s -1 and for hAgo2 & hPACT: k 1 : 18.6 (± 3.5) s -1 , k 2 : 0.13 (± 0.02) s -1 and k 3 : 0.01 (± 0.001) s -1 were determined. With the mutant hAgo2-PAZ9 the following rate constant were calculated: k 1 : 14.9 (± 2.7) s -1 , k 2 : 0.07 (±0.01) s -1 and k 3 : 0.01 (± 0.0009) s -1 in the presence of hTRBP and k 1 : 16.2 (± 0.6) s -1 , k 2 : 0.38 (±0.01) s -1 and k 3 : 0.007 (± 0.002) s -1 in the presence of hPACT.

Article Snippet: Data were fitted using a single exponential equation (Grafit 5, Erithacus Software).

Techniques: Labeling, Incubation, Mutagenesis